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Wu D, Mehdipour AR, Finke F, Goojani HG, Groh RR, Grund TN, Reichhart TMB, Zimmermann R, Welsch S, Bald D, Shepherd M, Hummer G, Safarian S. Dissecting the conformational complexity and mechanism of a bacterial heme transporter. Nat Chem Biol 2023:10.1038/s41589-023-01314-5. [PMID: 37095238 PMCID: PMC10374445 DOI: 10.1038/s41589-023-01314-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 03/14/2023] [Indexed: 04/26/2023]
Abstract
Iron-bound cyclic tetrapyrroles (hemes) are redox-active cofactors in bioenergetic enzymes. However, the mechanisms of heme transport and insertion into respiratory chain complexes remain unclear. Here, we used cellular, biochemical, structural and computational methods to characterize the structure and function of the heterodimeric bacterial ABC transporter CydDC. We provide multi-level evidence that CydDC is a heme transporter required for functional maturation of cytochrome bd, a pharmaceutically relevant drug target. Our systematic single-particle cryogenic-electron microscopy approach combined with atomistic molecular dynamics simulations provides detailed insight into the conformational landscape of CydDC during substrate binding and occlusion. Our simulations reveal that heme binds laterally from the membrane space to the transmembrane region of CydDC, enabled by a highly asymmetrical inward-facing CydDC conformation. During the binding process, heme propionates interact with positively charged residues on the surface and later in the substrate-binding pocket of the transporter, causing the heme orientation to rotate 180°.
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Affiliation(s)
- Di Wu
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt/Main, Germany
| | - Ahmad R Mehdipour
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt/Main, Germany
- Center for Molecular Modeling (CMM), Ghent University, Zwijnaarde, Belgium
| | - Franziska Finke
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt/Main, Germany
| | - Hojjat G Goojani
- Amsterdam Institute for Life and Environment (A-LIFE), AIMMS, Faculty of Science, Vrije University of Amsterdam, Amsterdam, the Netherlands
| | - Roan R Groh
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt/Main, Germany
| | - Tamara N Grund
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt/Main, Germany
| | - Thomas M B Reichhart
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt/Main, Germany
| | - Rita Zimmermann
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt/Main, Germany
| | - Sonja Welsch
- Central Electron Microscopy Facility, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Dirk Bald
- Amsterdam Institute for Life and Environment (A-LIFE), AIMMS, Faculty of Science, Vrije University of Amsterdam, Amsterdam, the Netherlands
| | - Mark Shepherd
- School of Biosciences, RAPID Group, University of Kent, Canterbury, UK
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt/Main, Germany
- Institute of Biophysics, Goethe University Frankfurt, Frankfurt/Main, Germany
| | - Schara Safarian
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt/Main, Germany.
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand.
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Frankfurt/Main, Germany.
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Futera Z, Wu X, Blumberger J. Tunneling-to-Hopping Transition in Multiheme Cytochrome Bioelectronic Junctions. J Phys Chem Lett 2023; 14:445-452. [PMID: 36622944 DOI: 10.1021/acs.jpclett.2c03361] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Multiheme cytochromes (MHCs) have attracted much interest for use in nanobioelectronic junctions due to their high electronic conductances. Recent measurements on dry MHC junctions suggested that a coherent tunneling mechanism is operative over surprisingly long long distances (>3 nm), which challenges our understanding of coherent transport phenomena. Here we show that this is due to (i) a low exponential distance decay constant for coherent conduction in MHCs (β = 0.2 Å-1) and (ii) a large density of protein electronic states which prolongs the coherent tunneling regime to distances that exceed those in molecular wires made of small molecules. Incoherent hopping conduction is uncompetitive due to the large energy level offset at the protein-electrode interface. Removing this offset, e.g., by gating, we predict that the transport mechanism crosses over from coherent tunneling to incoherent hopping at a protein size of ∼7 nm, thus enabling transport on the micrometer scale with a shallow polynomial (∼1/r) distance decay.
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Affiliation(s)
- Zdenek Futera
- Faculty of Science, University of South Bohemia, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic
| | - Xiaojing Wu
- University College London, Department of Physics and Astronomy, Gower Street, London WC1E 6BT, U.K
| | - Jochen Blumberger
- University College London, Department of Physics and Astronomy, Gower Street, London WC1E 6BT, U.K
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Sosna M, Ferapontova EE. Electron Transfer in Binary Hemin-Modified Alkanethiol Self-Assembled Monolayers on Gold: Hemin's Lateral and Interfacial Interactions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:11180-11190. [PMID: 36062334 DOI: 10.1021/acs.langmuir.2c01064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Orientated coupling of redox enzymes to electrodes by their reconstitution onto redox cofactors, such as hemin conjugated to self-assembled monolayers (SAMs) formed on the electrodes, poses the requirements for a SAM design enabling reconstitution. We show that the kinetics of electron transfer (ET) in binary SAMs of alkanethiols on gold composed of in situ hemin-conjugated 11-amino-1-undecanethiol (AUT) and diluting OH-terminated alkanethiols with 11, 6, and 2 methylene groups (MC11OH, MC6OH, and MC2OH) depends on both the SAM composition and surface density of hemin, Γheme. In AUT/MC11OH SAMs composed of equal linker/diluent lengths, the heterogeneous ET rate constant ks decreased with the Γheme and varied between 70 and 500 s-1. For shorter diluents, the ks of 245-330 s-1 (C6) and 300-340 s-1 (C2) showed a little (if any) Γheme dependence. In AUT/MC11OH SAMs, the increasing Γheme resulted in the steric crowding of hemin species and their neighboring lateral interactions in the plane of hemin localization, affecting the potential distribution at the SAM/electrode interface and inducing local electrostatic effects interfering with hemin oxidation. In AUT/MC6OH and AUT/MC2OH SAMs, hemin discharged at the plane of the closest approach to the gold surface, equal to the diluent length and permeable to electrolyte ions, which lessened those effects. All studied binary SAMs provided steric hindrance for protein reconstitution on the hemin cofactor conjugated to the extended AUT linker. Further use of SAM-modified electrodes with the covalently attached hemin as interfaces for heme proteins' reconstitution should consider SAMs with loosely dispersed redox centers terminating more rigid molecular wires. Such wires place hemin at fixed distances from the electrode surface and thus ensure the interfacial properties required for the effective on-surface reconstitution of proteins and enzymes.
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Affiliation(s)
- Maciej Sosna
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
| | - Elena E Ferapontova
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
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Somani A, Sander W. Reaction of electrons trapped in cryogenic matrices with benzophenone. J PHYS ORG CHEM 2022. [DOI: 10.1002/poc.4335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Ankit Somani
- Lehrstuhl für Organische Chemie II Ruhr‐Universität Bochum Bochum Germany
| | - Wolfram Sander
- Lehrstuhl für Organische Chemie II Ruhr‐Universität Bochum Bochum Germany
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Xiao L, Liu G, Gong F, Zhu H, Zhang Y, Cai Z, Li Y. A Minimized Synthetic Carbon Fixation Cycle. ACS Catal 2021. [DOI: 10.1021/acscatal.1c04151] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Lu Xiao
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guoxia Liu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Fuyu Gong
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huawei Zhu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanping Zhang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhen Cai
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yin Li
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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